Do we still need supertrees?

See research article http://www.biomedcentral.com/1741-7007/10/12 webciteAfter more than two centuries of intensive research the phylogeny of such important groups as the carnivores, let alone deeper phylogenetic relationships, is still not satisfactorily settled. Recently, Nyakatura and Bininda-Emonds [1] published an up-dated phylogeny of all 286 carnivore species. The new phylogeny is an extension of a study 12 years ago [2], which needed revision due to better methodologies and more data, especially DNA sequence data.However, the reconstruction of the carnivore tree is not as straightforward as one may expect. Typically, DNA or protein sequence data or phylogenies are available for only a subset of the carnivores. Thus, the major challenge is to construct one phylogeny for a taxonomic group from multiple sources. To this end the authors analyzed 241 trees available from the literature and additionally 74 gene trees generated from sequence data. The total of 341 so-called source trees was then combined into one supertree, assumed to mirror the phylogeny of the carnivore species. Combining trees derived from different data sets falls into the realm of supertree methods [3]. Alternatively one may also apply the so-called supermatrix method to combine data [4]. Here, the character data are pooled and then followed by a tree reconstruction. Both methods are in wide use and it is still an open question which method is preferable.Supertree methods combine source-trees, or trees obtained from the literature, with overlapping species sets into one tree. Nyakatura and Bininda-Emonds [1] selected matrix representation with parsimony (MRP) [5] as the method of choice for generating a supertree of carnivore species. The workflow is illustrated in Figure 1: MRP constructs a new data matrix (MRP-matrix), where each species in the source-trees is represented in a row. The columns of the MRP-matrix are built by encoding the source-trees. Species sharing a common node in the root